[David Shattuck]

Hi Emily –

Yes, please do.

thanks,
David

[David Shattuck]

Hi Emily –

I can’t quite picture what you have in mind — is there an image in a publication or online that is similar to what you are trying to make?

You might try using a cutting plane in the 3D view. You can turn toggle these using the x/y/z keys. E.g., for press x once to cut in the +x direction, a second time to cut in the -x direction, and a third time to turn off the cutting plane.

thanks,
David Shattuck

[David Shattuck]

hi Luca –

We are in the process of putting out a new release this week and will be updating our website to match. We’ll be updating the sections on tractography.

The option for multi-threading means that BrainSuite will run parallel jobs for finding the tracks. If you have a CPU with multiple cores, then this will speed up the computation. For example, if you have a quad-core hyperthreaded CPU, then BrainSuite will launch 8 threads for the computation, and it will be about 8 times as fast. One side effect of the parallel computation is that the order in which the tracks are found is non-deterministic. This is why we have the sort option — it reorders the tracks to be consistent with the single-threaded version. The track order probably has no effect on most applications, but it is useful if you want to compare processing, e.g., compare results from two different computers (we use this to test Mac vs. Linux vs. Windows).

Many of the other parameters may be dependent on your own data. The angle threshold controls how much the tracks can bend at each step, so how you set this may depend on the anatomy you are studying. Increasing it may produce extraneous tracks. The FA threshold is useful for constraining the tracking to the white matter when computing tracks in DTI; similarly, the the GFA/L2 threshold can be used when using the ODFs. You can use the mask tool to explore the effect of different thresholds on the boundaries in your image. For the FA threshold, you might try a range between 0.1 and 0.3.

thanks,
David Shattuck

[David Shattuck]

Hi –

The voxels in the mask are used to estimate parameters for bias field correction and tissue classification. The more accurately the mask represents the brain the better, the more data there are for these estimates. This is particularly important for the bias field, as it is spatially varying. You will get different results if you remove pieces of the cerebellum, but small errors in the mask probably won’t affect it too much.

thanks,
David Shattuck

[David Shattuck]

We have these tools in development/testing, but we haven’t released them yet. I’m hoping to include them with BrainSuite16a, which should be out in the next few weeks.

thanks,
David Shattuck

[David Shattuck]

What is the resolution of the images you are using?

Usually when this happens it is because the image has not been segmented properly by the preceding steps.

-David Shattuck

[David Shattuck]

hi Luca –

You can load tracks by using the menu (File -> Open -> Open Fiber Track Set) or dragging a .dft file onto the user interface.

thanks,
David Shattuck

[David Shattuck]

I haven’t seen this problem previously — can both of you let me know what operating system/version you are using?

thanks,
David

[David Shattuck]

Hi Joseph –

It looks like you are using OS X 10.6.8. The latest version of BrainSuite uses Qt 5.5.1, which only supports OS X 10.8 or greater. I think that is probably what is causing the problem.

thanks,
David

[David Shattuck]

Fucang –

Great! Glad to hear it’s working.

cheers,
David

[David Shattuck]

Hi Fcuang –

The BSS software has been updated with a fix for this issue. Can you try reinstalling and let us know if it worked?

thanks,
David Shattuck

[David Shattuck]

Hi Abujamea –

Great — happy to hear that solved the problem.

thanks,
David

[David Shattuck]

Hi Fcuang –

We have a currently testing a fix for this. We will update you on this once it is ready for download.

thanks,
David Shattuck

[David Shattuck]

Hi Nuua –

Just to clarify what you are trying to do : do you basically want to sample the BrainSuite generated tracks into an image volume? Are you looking for a simple binary mask or a tract density map?

We do have some code to do these things. The first is in Matlab, and you can download the source code here:

http://neuroimage.usc.edu/neuro/Resources/TractConnect

Will that provide what you need?

We also have some additional C++ command line tools for this that we haven’t released it publicly yet. I expect we will have those available in the next two weeks.

thanks,
David Shattuck

[David Shattuck]

Hi Abujamea –

It looks like a processing error happened earlier in the cortical surface extraction routine. Without seeing all of your output, my best guess is that the skull-stripping step didn’t remove a sufficient amount of the scalp/neck, which then resulted in a misclassification of GM during the tissue classification step.

Can you step through the processing steps for cortical extraction and see where if it failed there?

thanks,
David Shattuck

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